[Bioperl-l] OBOEngine does not have the function parse()

[Siddhartha Basu]

I think you have to use Bio::OntologyIO for input. Something like this

my $parser = Bio::OntologyIO->new(
                      -format    => "obo",
                      -file      => 'gene_ontology.1_2.obo');
my $ont = $parser->next_ontology;
say $ont->name;
my @roots = $ont->get_root_terms;
say $_->name for $ont->get_child_terms($roots[0]);

Hope this helps,
-siddhartha

On Fri, 31 Jan 2014, Fenglou Mao wrote:

> Dear all.
> 
> I am tring to run the code below:
>   use Bio::Ontology::OBOEngine;
> 
>   my $parser = Bio::Ontology::OBOEngine->new
>         ( -file => "gene_ontology.1_2.obo" );
> 
>   my $engine = $parser->parse();
> 
> 
> I got an error message:
> Can't locate object method "parse" via package "Bio::Ontology::OBOEngine" at ./GO4.pl line 12.
> 
> I checked the source code, it seems this function "parse" cannot be found anywhere.
> Any idea? My BioPerl version is 1.6.901
> 
> Fenglou
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